SMED30033816

Overview
NameSMED30033816
Smed IDSMED30033816
Length (bp)572
Neoblast Clusters

Zeng et. al., 2018




 



 

Overview

 

Single cell RNA-seq of pluripotent neoblasts and its early progenies


We isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each cluster’s gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq.

We also tested sub-lethal irradiation exposure. To profile rare pluripotent stem cells (PSCs) and avoid interference from immediate progenitor cells, we determined a time point after sub-lethal irradiation (7 DPI) with minimal piwi-1+ cells, followed by isolation and single-cell RNA-seq of 1,200 individual cells derived from X1 (Piwi-1 high) and X2 (Piwi-1 low) cell populations (Sub-lethal Irradiated Surviving X1 and X2 Cell Population)




Explore this single cell expression dataset with our NB Cluster Shiny App




Embryonic Expression

Davies et. al., 2017




Hover the mouse over a column in the graph to view average RPKM values per sample.
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Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult.
For further information about sample preparation and analysis for the single animal RNA-Seq experiment, please refer to the Materials and Methods

 

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Anatomical Expression

PAGE et. al., 2020




SMED30033816

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30033816SMESG000081807.1 SmedASXL_069448SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30033816 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.007765:14082..14653 -2761
v31.009197:11258..11829 -2617
v31.007145:25649..26220 -2617
v31.004231:30823..31394 -2617
v31.010619:6409..6980 -2599
v31.009246:3903..4463 -2598
v31.002062:37553..38118 -2557
v31.012523:7880..8439 -2499
Homology
BLAST of SMED30033816 vs. Planmine SMEST
Match: SMESG000030754.1 (SMESG000030754.1)

HSP 1 Score: 265.774 bits (678), Expect = 1.862e-89
Identity = 161/179 (89.94%), Postives = 167/179 (93.30%), Query Frame = 1
Query:   34 MGSSRRLSLRQASEEIQRWLDNXXXXXXXXXXXXXXXLDTSSVAEDIIENESDHQSEFSGYESEIEQPFAADYLSKDGKVQWSHNPLSSAQGRRSKHNVVKVTRAVVLGGKSMNDPCESVQXXXXXXXXXXXXKHTNEELGQRR*STAEKNPKYLDDFTIVEMKAAVGIMILVGVMCSK 570
            M SSRRLSLRQASEEIQRWL NDDDD SEADASGGESLDTSSVAEDIIENESDHQSEFSGYESEIEQPFAADYLSKD KVQWS NPLSSAQGRRSKHN V VTRAV LGGKS+NDPC SV+LFLDDWFF+ LLKHTNEELG+RR STAEK+PKYL+DFTIVEMKAAVGIMILV VMCSK
Sbjct:    1 MVSSRRLSLRQASEEIQRWLYNDDDDESEADASGGESLDTSSVAEDIIENESDHQSEFSGYESEIEQPFAADYLSKDEKVQWSQNPLSSAQGRRSKHNAVNVTRAVFLGGKSVNDPCGSVKLFLDDWFFDKLLKHTNEELGRRRQSTAEKDPKYLEDFTIVEMKAAVGIMILVDVMCSK 179          
BLAST of SMED30033816 vs. Planmine SMEST
Match: SMESG000081807.1 (SMESG000081807.1)

HSP 1 Score: 88.5817 bits (218), Expect = 1.542e-20
Identity = 42/46 (91.30%), Postives = 44/46 (95.65%), Query Frame = 1
Query:  433 KHTNEELGQRR*STAEKNPKYLDDFTIVEMKAAVGIMILVGVMCSK 570
            KHTNEELG+R  STAEK+PKYLDDFTIVEMKAAVGIMILVGVMCSK
Sbjct:    8 KHTNEELGRRGQSTAEKDPKYLDDFTIVEMKAAVGIMILVGVMCSK 53          
The following BLAST results are available for this feature:
BLAST of SMED30033816 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30033816 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30033816 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30033816 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30033816 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30033816 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30033816 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30033816 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30033816 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30033816 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30033816 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30033816 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30033816 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30033816 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000030754.11.862e-8989.94SMESG000030754.1[more]
SMESG000081807.11.542e-2091.30SMESG000081807.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30033816 ID=SMED30033816|Name=SMED30033816|organism=Schmidtea mediterranea sexual|type=transcript|length=572bp
TGCAGCAATATTTGTAACGTTTGTGGCTTTTAGATGGGGTCATCAAGACG
ATTATCACTAAGACAAGCATCAGAAGAAATACAAAGGTGGCTTGATAACG
ACGACGATGACGGGAGTGAAGCTGATGCATCCGGAGGGGAAAGTTTGGAT
ACAAGTTCCGTAGCAGAAGACATCATTGAGAATGAAAGCGACCATCAATC
CGAGTTCAGCGGTTATGAATCAGAAATTGAGCAGCCATTTGCAGCAGACT
ACCTATCAAAGGATGGAAAAGTCCAGTGGTCACATAATCCATTGTCATCA
GCACAAGGTAGACGTTCAAAACACAATGTTGTAAAGGTCACACGAGCTGT
TGTTCTTGGTGGCAAGAGTATGAATGATCCTTGCGAAAGTGTTCAACTTT
TCCTGGATGACTGGTTTTTTGAATAGCTTTTGAAGCATACTAATGAGGAA
TTGGGGCAACGCAGGTAGTCAACAGCTGAGAAAAATCCGAAATATCTTGA
TGACTTTACCATTGTTGAAATGAAAGCAGCAGTTGGTATCATGATACTTG
TTGGCGTGATGTGCTCAAAGAG
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protein sequence of SMED30033816-orf-1

>SMED30033816-orf-1 ID=SMED30033816-orf-1|Name=SMED30033816-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=131bp
MGSSRRLSLRQASEEIQRWLDNDDDDGSEADASGGESLDTSSVAEDIIEN
ESDHQSEFSGYESEIEQPFAADYLSKDGKVQWSHNPLSSAQGRRSKHNVV
KVTRAVVLGGKSMNDPCESVQLFLDDWFFE*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..29
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..50